Let KAYAK do the searching
Based on KAYAK hotel searches, the most popular destination is Little Current (40% of total searches to Manitoulin Island). The next most popular destinations are Gore Bay (28%) and Mindemoya (23%). Searches for hotels in Manitowaning (9%) are also popular.
KAYAK users have found double rooms in Manitoulin Island for as cheap as $95 (Mindemoya) in the last 3 days. The average price is $141.